


Vengeance Is Mine

by WillSherJohnKhan



Category: Sherlock (TV), Star Trek Into Darkness - Fandom
Genre: A bit of angst (all right maybe more than a bit), Alternate ending to Star Trek: Into Darkness, F/M
Language: English
Status: In-Progress
Published: 2016-11-15
Updated: 2017-06-12
Packaged: 2018-08-31 03:27:25
Rating: Not Rated
Warnings: Graphic Depictions Of Violence
Chapters: 2
Words: 2,894
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/8561803
Author URL: https://archiveofourown.org/users/WillSherJohnKhan/pseuds/WillSherJohnKhan
Summary: In the confusion of Admiral Marcus’ attack on the Enterprise, Khan has escaped from the Medical Bay, kidnapping Molly Hooper along the way, before transporting across to the Vengeance where he kills Admiral Marcus and his crew.He is about to destroy the badly damaged Enterprise when Molly attempts to convince him to spare them their lives, and instead just leave and find somewhere where he can begin a new life...with her.In celebration of 50 years of Star Trek 1966-2016Disclaimer:I don’t own any of these characters. I just like to play with them every now and then.





	1. Shall We Begin...

**Author's Note:**

> There are a couple of things that need to be noted:  
> 1\. This story is clearly an Alternate Universe version of Star Trek: Into Darkness. In this version Scotty remained on the Enterprise, Carol Marcus isn’t part of this story, and Molly Hooper appears as an Ensign.  
> 2\. FAIR WARNING: If when you read this story, there are some quite large familiar chunks in it, there’s a reason. I’m using the novelisation of Star Trek: Into Darkness, by Alan Dean Foster as well as trailers and TV spots for the film that included dialogue that did not appear in the film to help tell my story. Some I have tweaked to suit the story.There was such a wealth of information that it seemed a shame not to borrow it.

***

Captain Kirk had ordered that the communication between himself and the unmarked Starfleet vessel be broadcast ship-wide…

*

USS ENTERPRISE – BRIDGE / VENGEANCE – BRIDGE

“Captain Kirk.”

“Admiral Marcus, I wasn’t expecting you. That’s some ship.”

“And I wasn’t expecting to get word that you’d taken Harrison into custody in violation of your orders. Or did you forget that you were directed to find him and take him out? The orders I gave you were simple and straightforward, so what went wrong?”

“The unexpected happened, sir. Not something to be dismissed lightly, when one considers our present location. We had to improvise when we experienced a warp core malfunction… But you already knew that, didn’t you, sir.”

“I don’t take your meaning.”

“Well that’s why you’re here, isn’t it? To assist us with repairs? Why else would the head of Starfleet personally bring a ship to the edge of the Neutral Zone?”

“Captain, they’re scanning our ship.”

“Did you hear that, Admiral? Having a quiet look around? Something I can help you find, sir?”

*

Throughout the ship its crew listened intently. What had originally sounded like a rescue mission had very quickly turned ominous.

*

USS ENTERPRISE – BRIDGE / VENGEANCE – BRIDGE

“Where’s your prisoner, Kirk? Tell me where you’re holding Harrison, and drop your shields so we can beam him over. I’m superseding your authority as of now.”

“No need for that, sir. As the captor of record, it’s my duty and responsibility to maintain control of the prisoner until he can be turned over to the appropriate authorities, all as per Starfleet regulations. The fact that I’m familiar with his crimes changes nothing. I’m preparing to return Khan to Earth for trial, sir… I would hope we can proceed with your understanding. I assure you that the prisoner is being well looked after and is completely under our control… We didn’t even have to fire so much as a single one of the ‘new’ torpedoes at him.”

“Well, shit. You talked to him. That was exactly what I was hoping to spare you from.”

“Spare me?”

*

The mood throughout the ship became increasingly unsettled as Marcus’ description of John Harrison / Khan went from ‘prisoner’, to ‘criminal’, to ‘war-lord’, to ‘creature’ as he desperately attempted to justify the need to cover up his actions since awakening Khan, blackmailing him into using his advanced intellect to develop weapons for Section 31.

*

USS ENTERPRISE – BRIDGE / VENGEANCE – BRIDGE

“I’ll have the entire incident expunged from the official records, and Khan and his crew will be disposed of quietly, no-one needs to know… Now I’m asking you, give him to me so I can end what I started.”

“He’s in Engineering, sir, under heavy guard awaiting continued questioning. But I’ll have him moved to the transporter room right away.”

“Thank you, son. I’ll take it from here.”

And the transmission ended.

Immediately after the Enterprise went to warp.

*

USS ENTERPRISE – MEDICAL BAY

The man to whom the conversation had revolved appeared oblivious to the commotion around him.

He sat on the bio-bed, back ramrod straight, with his hands manacled, surrounded by guards who never took their eyes off him. Khan sat quietly, his expression blank, deep in thought and gazing at nothing in particular.

If he were honest with himself, Dr. McCoy found Khan’s lack of response a little unnerving.

Bones studied the man before him, and he wondered to himself, ‘if you peeled back the layers of personality, of emotion, what might one find? A murderous maniac or a man wronged by not one but two societies his own of three centuries ago, and today’s as represented by Alexander Marcus?’

“Well at least we’re moving again,” McCoy pointed out conversationally as he passed a tri-corder over the prisoners face.

From where he was seated, Khan lifted his gaze to meet that of the doctor. “If you think you’re cleanly away, if you think you’re safe at warp – you’re wrong.”

McCoy just grunted at the prisoners reply. However, when moments later the Enterprise was struck by a phaser blast strong enough to knock them out of warp, leaving the ship adrift, like a sitting duck, at the mercy of the far larger and more heavily armoured Vengeance. The doctor was forced to concede the truth of Khan’s statement.

Not that Khan cared. 

At that moment his attention was focussed on the reactions of the crew to their current situation, and most particularly that of the security detail assigned to watch him. As concern turned to panic, his patience was rewarded when even the most hardened individuals, like those who guarded him wavered, if only for a moment.

But that was all Khan needed.

In the blink of an eye he went from coolly disinterested prisoner to a determined fighting machine, using a combination of speed, strength and skill that guaranteed his security detail never knew what hit them. A single blow with his manacled wrists knocked Hendorff out cold. Before the others could react Khan had overpowered them with a series of precisely-timed blows: a squeeze to the neck, a twist of an arm, and a slam to the side of the head to render them equally unconscious. Before tossing their limp bodies as though they weighed nothing, to the floor, against a wall, or into any unfortunate medical staff who happened to be in the way.

*

It was at that very moment that Ensign Molly Hooper chose to enter the Medical Bay. Whatever had brought her there was instantly forgotten as she witnessed the carnage Khan was inflicting. But in the time it took her to enter, see what was going on and make the decision to leave, Khan had removed the heavy-duty handcuffs, acquired a weapon, and taken her hostage.

*

Only a few futile attempts were made to intercept them however, as the Enterprise was currently under attack. Admiral Marcus having decided to destroy all evidence of his misdeeds in one foul swoop. So with everyone more concerned with there own survival, resistance to Khan’s escape plan was minimal.

Khan held Molly securely, his arm wrapped around her waist, her back plastered to his chest as he moved quickly and confidently through the ship. His superior reflexes guaranteeing he stayed upright as the Enterprise continued to be bombarded by the Vengeance’s impressive weapons array.

Molly did her best to escape the clutches of the incredibly good-looking, yet frightening man who held her. But Khan brought her feeble attempts to an end, with the quick application of pressure to her neck. As her body slumped, Khan easily caught her before slinging her over his broad shoulder.

He then continued to his destination.

*

USS ENTERPRISE – ENGINEERING

With everyone in engineering focussed on trying to get the warp drive up and running, no one paid Khan any attention.

Through the unchecked conversations he’d overheard while in the ship’s brig, Khan learned that Chief Engineer Scott had found his portable trans-warp-beaming device, and had very conveniently brought it with him onto the Enterprise.

After a quick search Khan found where it had been stored. And then with lightening fast speed he’d re-set the transport co-ordinates. 

Moments later he and Molly disappeared off the Enterprise…

***

VENGEANCE - BRIDGE

… To re-materialise on the bridge of the Vengeance.

Whatever confidence Alexander Marcus was feeling immediately evaporated when Khan materialised on the bridge.

After depositing the unconscious Molly to the floor, Khan, with military efficiency and extreme prejudice used his enhanced abilities to deal with the mercenaries that made up the Vengeance’s minimal crew.

The only sounds on the bridge were the snapping of bones, followed by the ominous thud of dead bodies hitting the deck.

The speed with which the feat was achieved was simply mind blowing, and it left the admiral in a state of stunned horror as he observed the bodies that littered the pristine bridge.

As Khan stormed towards his nemeses, Marcus, realising the danger he was in made to get up, but Khan was on him before he could get to his feet.

Trapped within the confines of the Captain’s chair there was no-where for the admiral to go, Khan had him well and truly cornered. Before Marcus could open his mouth to bargain for his life, Khan had taken hold of the admiral’s head in both his hands and began to squeeze.

Over the admiral’s screams and the sound of cracking bones, Khan told him. “You should have let me sleep.”

But Marcus could make not reply. Nor would he ever do so again.

Tossing the admiral’s body to the floor, Khan took his place in the Captain’s chair. With a flick of the controls on the chairs armrest, he soon had communications open with the badly damaged Enterprise.

***

VENGEANCE – BRIDGE / USS ENTERPRISE – BRIDGE

“I’ll make my demands very simple, Captain. Give me my crew.”

Kirk and Spock exchanged a look.

“That’s, going to be a problem,” Kirk responded.

Khan used his instruments to scan the Enterprise.

“Your transporters are down,” he noted. “Fortunately that’s not a problem, as mine are fully functional.”

Another look was exchanged between Captain and First officer.

“That’s not the only problem.”

“This meaningless banter is pointless,” Khan stated, becoming clearly annoyed. “Give me my crew.”

“We can’t,” Kirk replied through gritted teeth.

Something about the captain’s expression left the augment uneasy.

“Where are my crew, Kirk?”

Spock stepped up next to his captain. “After we removed your crew from the torpedoes, their cryotubes were moved to the cargo bay…”

“Which sustained a direct hit,” Kirk finished.

“You’re lying,” Khan snarled.

“Your ships instruments are fully functioning, check for yourself,” Kirk advised.

As Khan scanned the Enterprise his anger faded and for a brief moment was replaced by grief, as the Vengeance’s instruments confirmed what Kirk had told him. The telltale signatures that represented the 72 members of his crew no longer existed.

They were gone.

He had fought so hard to be reunited with his crew, his family, only to fail…

“I am sorry,” Kirk said with genuine regret.

But Kirk’s sympathy only reignited Khan’s loathing for Starfleet, and everything it represented.

***

VENGEANCE – BRIDGE

Khan had designed the dreadnaught-class warship to be fully automated so that a minimal crew could man it, one if necessary. It was bigger, faster and more heavily armed than any ship currently in service at Starfleet.

Its firepower was further enhanced when Khan imputed the co-ordinates into the warship’s military-grade transporter system, and began retrieving the 72 torpedoes from the Enterprise’s to the Vengeance’s torpedo bay.

Then without further delay he gave the order. “Computer, arm torpedoes.”

“Torpedoes armed.” Vengeance’s computer immediately responded.

Before he could complete his order, a desperate, frightened voice called out. “You can’t!”

Molly had regained consciousness in time to witness Admiral Marcus’ demise. She remained where she was, observing the confrontation between Khan and the Enterprise. But when she realised his intention, she knew she could no longer remain a bystander.

Khan turned his head and coolly observed the young woman he had made his prisoner. “And why is that?”

***


	2. A Moment Suspended In Time

**Summary for the Chapter:**

> Disclaimer:  
> I don’t own any of these characters. I just like to play with them every now and then.

***

VENGEANCE – BRIDGE 

“Well...” Molly began, her explanation abruptly interrupted when with lightening speed Khan moved. One moment he was seated in the Captain’s Chair and the next he was looming over her, the epitome of an avenging angel, dark, menacing and brooding. Driven with a determination to cause as much death and destruction as possible.

And given the number of dead bodies that littered the bridge he’d made a more than reasonable start.

But the wanton loss of life, the memory of Admiral Marcus’ tortured screams, even the threat to the Enterprise and her crew were temporarily forgotten as the young ensign gazed up at her abductor, the man formally known as Commander John Harrison.

Apart from his fringe that had fallen rather endearingly into his aqua coloured eyes, he was all alpha male. A warrior, trained to fight and to kill whenever he felt himself trapped or under threat. The incredibly well-toned body: broad chest and shoulders, impressive biceps, rigidly inflexible abs, long elegant fingers that extended from hands capable of squeezing the very life from those he proclaimed his enemy. Even his muscles as they flexed impatiently, straining to break free from the tight-fitting off-duty undershirt he wore. Not to mention the narrow hips, powerful thighs and legs that seemed to go on forever encased within the equally snug-fitting trousers that left absolutely nothing to the imagination.

Everything from head to toe loudly proclaimed him a primordial, potent and predatory male

When her gaze once again became a captive to his now piercing steel-coloured eyes, Molly had the uncomfortable feeling that he had the ability to see right through her. That he could so easily strip her of all her defences, laying her wayward thoughts completely bare. 

*

Khan watched the young ensign in cool amusement, well aware of the affect he was having on her. He had observed that same reaction he could see so clearly reflected in her eyes more times than he cared to count, both in his own time and that of the alien future he now found himself.

The difference now was that her reaction wasn’t based on any intention to align herself with him to gain power or political advantage. She had no idea who he really was, nor what he had been and what that had meant in his time.

She was reacting purely on instinct, completely incapable from hiding how she felt from him. Her body almost vibrating with expectation as it sensed the irresistible pull of his carnal masculinity that called to her, urging her to surrender. The delicate flush to her cheeks, the escalation of her breathing and the dilation of her pupils all told him exactly what she wanted.

And he was not the least averse to exploiting those needs for his own purposes.

Yes, he nodded to himself. Here was an opportunity. He would have her, would enjoy taking his pleasure as he took his fill of her, but only for as long as he had need of her. Then he would discard her, as he had with all the others.

*

His ability to seduce her without saying a word had made Khan supremely confident that the young ensign would now willingly do his bidding, and so he allowed a self-satisfied smirk to settle on his plump cupids-bow lips.

This was a mistake.

As soon as Molly’s subconscious registered the cruel twist to his sensuous lips, it snapped her out of the hypnotic spell he had cast over her.

No longer blind to his intention to manipulate her, Molly’s response was instantaneous.

The stinging sensation as her delicate hand made contact with his finely chiselled cheekbone was completely unexpected. His shocked expression filled Molly with immense satisfaction at the knowledge that he had not seen it coming.

Looking down at the young woman before him, Khan realised how clearly he had underestimated her. Small she may be, but there was a fierce determination to her that he had arrogantly overlooked, preferring to lump her in the same category as every other woman he had ever known.

Rubbing his injured cheek he took careful inventory of the woman before him.

There was nothing particularly remarkable about her appearance. She was small, around 5”4’. Her eyes and her hair, pulled back in a practicable ponytail were brown in colour. She reminded him of a sparrow, simple, plain and common, but endearing.

That analogy unexpectedly sparked a range of conflicting emotions within the augment.

Before when he had wanted to take, it had only been to use her. Now he was overpowered by something far stronger 

Khan’s gaze hungrily took in her dainty features. His eyes travelled slowly over her petite figure as his thoughts became more predatory, which was matched by the smile that now graced his lips.

She was nothing like what usually attracted him to a woman. But something about her called to a part of him that he’d only allowed those he’d just lost to reside. Her goodness, her kind heart and her innocence were having a disturbing affect on him.

He felt an unexpected need to protect her.

Confused by these unexpected and contradictory feelings, Khan used them to refuel his rage over what Alexander Marcus had done to him. And so he rounded on her, declaring between clenched teeth as he pointed towards the view-screen, where the Enterprises Command Crew were still visible. “Your Commanders have committed a crime I cannot forgive.”

His loathing of Starfleet and everything it stood for was plain to see. And yet Molly could see through his intense anger, to the pain and the sense of loss he was feeling, and her heart broke for him.

She didn’t know the full story, but from the little she’d heard from the ship-wide broadcast the admiral had clearly gone against much of what Starfleet stood for, and had been prepared to go to murderous lengths to cover his tracks. She didn’t know how, but she knew she had to make Khan understand that one man’s actions did not represent the organisation as a whole.

With quiet determination Molly stepped towards him, so that they were once again toe to toe. She looked up into his stormy eyes and noted calmly. “Except they didn’t”

Khan raised an elegant eyebrow “Really?” came back his cool response. “I beg to differ.”

***

**Notes for the Chapter:**

> There was actually going to be a lot more to this chapter, but as I started writing it this one little scene wanted all the attention. So I put the rest of my notes aside for the time being and will add them to the next chapter. :-)

**Author's Note:**

> As always, Kudos and Comments are most welcome.


End file.
